diff tools/mira4/mira4_mapping.xml @ 13:7fcabeeca5df draft

Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong

--- a/tools/mira4/mira4_mapping.xml	Mon Feb 03 06:25:35 2014 -0500
+++ b/tools/mira4/mira4_mapping.xml	Sun Feb 16 16:30:48 2014 -0500
@@ -80,9 +80,11 @@
         <configfile name="manifest">
 project = MIRA
 job = mapping,${job_type},${job_quality}
-parameters = -GE:not=1 -NW:cmrnl -DI:trt=/tmp
+parameters = -NW:cmrnl=no -DI:trt=/tmp
 ## -GE:not is short for -GENERAL:number_of_threads and using one (1)
 ## can be useful for repeatability of assemblies and bug hunting.
+## This is overriden by the command line -t switch which is easier
+## to set from within Galaxy.
 ##
 ## -NW:cmrnl is short for -NAG_AND_WARN:check_maxreadnamelength
 ## and without this MIRA aborts with read names over 40 characters
@@ -128,12 +130,15 @@
 #end if
 ##Record the segment placement (if any)
 #if str($rg.segments.type) == "paired"
-segmentplacement = ${rg.segments.placement}
-segmentnaming = ${rg.segments.naming}
+segment_placement = ${rg.segments.placement}
+segment_naming = ${rg.segments.naming}
 #end if
-#if str($rg.segments.type) == "none"
-segmentplacement = ?
-#end if
+##if str($rg.segments.type) == "none"
+##MIRA4 manual says use segment_placement = unknown or ? for unpaired data
+##but this stopped working in MIRA 4.0 RC5 and 4.0 (final). See:
+##http://www.freelists.org/post/mira_talk/Unpaired-reads-and-segment-placement--or-unknown
+##segment_placement = ?
+##end if
 ##MIRA will accept multiple filenames on one data line, or multiple data lines
 #for $f in $rg.filenames
 ##Must now map Galaxy datatypes to MIRA file types...